5WRC

Crystal structure of proteinase K from Engyodontium album


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Hydroxyethyl cellulose matrix applied to serial crystallography

Sugahara, M.Nakane, T.Masuda, T.Suzuki, M.Inoue, S.Song, C.Tanaka, R.Nakatsu, T.Mizohata, E.Yumoto, F.Tono, K.Joti, Y.Kameshima, T.Hatsui, T.Yabashi, M.Nureki, O.Numata, K.Nango, E.Iwata, S.

(2017) Sci Rep 7: 703-703

  • DOI: 10.1038/s41598-017-00761-0
  • Primary Citation of Related Structures:  
    5WRA, 5WRC, 5WRB, 5WR9, 5WR8

  • PubMed Abstract: 
  • Serial femtosecond crystallography (SFX) allows structures of proteins to be determined at room temperature with minimal radiation damage. A highly viscous matrix acts as a crystal carrier for serial sample loading at a low flow rate that enables the ...

    Serial femtosecond crystallography (SFX) allows structures of proteins to be determined at room temperature with minimal radiation damage. A highly viscous matrix acts as a crystal carrier for serial sample loading at a low flow rate that enables the determination of the structure, while requiring consumption of less than 1 mg of the sample. However, a reliable and versatile carrier matrix for a wide variety of protein samples is still elusive. Here we introduce a hydroxyethyl cellulose-matrix carrier, to determine the structure of three proteins. The de novo structure determination of proteinase K from single-wavelength anomalous diffraction (SAD) by utilizing the anomalous signal of the praseodymium atom was demonstrated using 3,000 diffraction images.


    Organizational Affiliation

    Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proteinase KA279Parengyodontium albumMutation(s): 0 
Gene Names: PROK
EC: 3.4.21.64
Find proteins for P06873 (Parengyodontium album)
Explore P06873 
Go to UniProtKB:  P06873
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PR
Query on PR

Download CCD File 
A
PRASEODYMIUM ION
Pr
WCWKKSOQLQEJTE-UHFFFAOYSA-N
 Ligand Interaction
NO3
Query on NO3

Download CCD File 
A
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.6α = 90
b = 68.6β = 90
c = 108.8γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrystFELdata processing
CrystFELdata scaling
Cootmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-11-29
    Type: Initial release
  • Version 1.1: 2018-01-31
    Changes: Data collection